Blue and Orange Morality: It quickly becomes clear, explicitly so in False Masks, that ponies do not subscribe to the same Laws of Magic that keep White Council wizards on the straight and narrow. Twilight Sparkle frequently performs spells that would call for her execution on Earth.
Discussed in-story, as while Twilight may be violating the letter of the Laws of Magic, the reasoning behind why those Laws exist in the first place is still being adhered to.
HAD to Be Sharp: The ponies come to realize that Harry's world requires a certain degree of ruthlessness in order for one to survive as well as to enable good to win, and Luna applies this to humans as a whole, one of the reasons the Humans Are the Real Monsters trope is averted, as detailed below.
Humans Are the Real Monsters: Nicely averted. There's the requisite shock over Dresden eating meat, but the Mane 6 grow to like him fairly easily. Luna and Celestia even say humanity seem to be a noble race, going by his example, and from what they saw of early Christians last time they visited Earth.
Knight in Sour Armor: Likewise with Harry, Twilight got an overview of his personality through the Soulgaze. Unlike Harry, she was terrified by what she saw. She saw him as a knight fighting a near endless horde of monsters, never once backing down. A knight who was more in danger of losing himself than losing to the horde.
"No. I don’t accept this." I rolled my eyes and crossed my arms. "A wizard from another dimension happens to open a gateway into a magical land filled with talking ponies, and the first one he meets just happens to be the holder of an ancient and sacred power. Then those two and her friends, who also bear these powers, must rescue somebody she cares about from a jealous rival? Are you kidding me? If Kirby did that in Arcanos, I’d walk out! That’s the plot of a crappy fantasy novel!"
And another one:
Twilight Sparkle: "What, you're just going to ignore it? The Elements are the foundation on which all of Equestria is built." Harry: "Yes. I’m very good at ignoring things. Watch in awe as I ignore the fact that Pinkie’s cupcake launcher is way too big to fit in her saddlebags, for instance."
Harry nearly Soulgazes Princess Celestia by accident, only for some unknown force to stop him. He's not even sure if the force did it for her protection or for his, but it still serves as a reminder that Celestia is not like him.
Morality Chain: The ponies become this for Harry, especially Twilight and Fluttershy.
Physical God: Harry meets Celestia and describes her as being as powerful and graceful as a Lady of the Fae Court, minus the scary. He is absolutely impressed when he learns that Twilight is her student. Luna, for obvious reasons, isn't quite as powerful, but he can sense that she still is miles above him. They get on smashingly.
Innocent Innuendo: Subverted in "Foolish Mistake". Twilight overhears Dresden and Rarity having an extremely suggestive conversation in her guest room and wants to assume the obvious, but figures that she's probably reading too far into it. That is, until Rarity blurts out "Oh, [Dresden]! This is the best sex I’ve ever had!".Double Subverted when Twilight breaks in and discovers that Dresden and Rarity weren't having sex, and weren't even in the room at all. Bob was mimicking their voices to troll Twilight.
Marty Stu: Invoked in "Holiday Present". Harry gains the 7th element of harmony, courage, and uses it to defeat Nightmare Chrysalisombra and save the Mane Six. Afterwards he proposes marriage to Twilight, and she accepts. As it turns out, the whole sequence is a fanfic-within-a-fanfic written by Harry's daughter.
The Quiet One: "Kindred Spirits" celebrates this trope by having the representatives from both franchises, McAnally and Big Macintosh, meet up and exchange a few words (the key word being "few") over drinks.
Added Alliterative Appeal: Harry gets chewed out by Twilight in this manner. He can't decide whether it's cute or terrifying until she follows it up with a near-Fluttershy-level Death Glare.
Batman Gambit: After failing to defeat Trixie, Twilight Sparkle appeals to her ego, tricking her into defeating herself.
Berserk Button: Pinkie becomes enraged when the Dark and All Powerful Trixie severely injures Rainbow Dash. Harry himself gets set off by women or children being threatened and people/ponies trying to brainwash him.
Blind Jump: This is how the whole story starts: Dresden is being chased by monsters through the Nevernever (a sort of shadow dimension between Earth and the worlds of The Fair Folk), and has to randomly exit to escape.
Book Ends: As with the first canon novel, Harry's narrative starts and ends with 'My Name is Harry Blackstone Copperfield Dresden'
Carnivore Confusion: Harry is smart enough to avoid any blunders in this field but still faces a difficult moment when Rarity inquires about the origins of his leather coat.
Curb-Stomp Battle: When Harry's possessed by the Nightmare, he flattens the Mane Cast in a physical confrontation. The spiritual confrontation, on the other hand...
When he meets Luna, he's struck by how adorkable and LOUD she is.
Demonic Possession: The Nightmare, the same demon that turned Luna into Nightmare Moon, possesses Trixie and aids her in petty revenge on Twilight and the others. After they beat it, it possesses Harry and turns him against them, until he sees through its mental manipulations and finally destroys it for good.
Death Glare: Before his soul gaze kicks in, Harry finds himself on the recieving end of Fluttershy's stare. It is not entirely clear which one Twilight is saving when she makes the two break eye contact.
Determinator: They all take turns, but Rainbow Dash and Applejack take the cake when trying to defuse the wall trap.
Trixie: I hope you all enjoyed that little glimmer of hope while it lasted, because those snakes have enough power in them to destroy anypony.
Applejack: Good thing I ain’t just anypony, then.
Rainbow Dash: Yeah. Equestria’s best flier isn’t gonna stop just because of some little bug zapper!
Dwindling Party: Invoked and defied. Trixie lures the group into her traps exactly for this purpose, but Harry and the Mane Six push their powers and skills to the limit to keep everypony alive.
Easily Forgiven: Harry shows concern when this happens after his Demonic Possession but Twilight tells him not to worry about it. He held back while possessed and ultimately fought back against the Nightmare, after all. That counts for something.
Exact Words: Harry uses the names of the Mane Six to prevent them from moving, but not from using magic.
Family-Unfriendly Violence: Due to the Cerebus Syndrome, the Mane Cast walk away from this adventure with much more severe injuries than they do in the show. Rainbow Dash, Pinkie Pie, and Twilight Sparkle get the worst of it, with Rainbow and Twilight being on the receiving end of a Flechette Storm and Pinkie being poisoned.
Foreshadowing: In-universe. Harry notices that Twilight's magic shield protects not just against kinetic force, but heat as well. He idly considers beefing up his own shield in the future, but apparently forgets, since "Strange Friends" takes place right before The Dresden Files novel Blood Rites, in which flamethrower-wielding vampires cripple one of Harry's hands when his shield fails to protect it from the effects of convection.
Full Body Disguise: Twilight uses an illusion spell to disguise Dresden as one of Celestia's guards when he's in public.
Green-Eyed Monster: Luna has a bit of this when she learns that Harry forced out and killed the Nightmare, something she was unable to do on her own. Harry tells her that Twilight made it sound much easier than it really was and that if the Mane Six hadn't been there, he'd be a goner.
Twilight realizes she's a bit jealous when she discovers that Harry's magical power exceeds hers, but quickly gets over it.
This becomes a Heartwarming Moment when Harry gives Twilight his full name, showing an impressive amount of faith in the pony.
I'm Having Soul Pains: Trixie shattering the Elements of Harmony to summon the Nightmare has the side effect of inflicting crippling pain on the Elements' bearers. Trixie even chooses the order in which each bearer is struck down so as to cause the most distress among the party. She starts with Fluttershy.
"Meanwhile at Fluttershy's house!" Pinkie Pie announced proudly. Fluttershy and I just looked at her. Fluttershy had apparently learned better than to ask, but I couldn't help myself. "Sorry, what?" Not that much of what she'd said had made any sense so far. But hey, a guy can hope, can't he? "Nothing, just setting up a scene transition." Pinkie's smile took up more of her face than I think was physically possible.
A telekinetic blast can be deadly when used to throw sharp objects. Also, the Elements of Harmony — they never cause direct harm, but that's still a lot of magic for Harry to channel into a fire spell. Celestia is not amused.
Mind Rape: The first thing Harry does after arriving in Equestria is accidentally soulgaze Twilight Sparkle.
Mood Whiplash: Used extensively, but particularly when Pinkie Pie invokesRule of Funny to appear in the room with the mane cast after holding back the hornets. She collapses from poison seconds later and would have died on the spot if Harry didn't react quickly.
More than Mind Control: This is how the Nightmare influences its hosts. It offers suggestions and temptations based on their darker impulses, then helps them plan when carrying those suggestions out.
Royals Who Actually Do Something: While everyone else is out adventuring to save the day, Celestia notices something is up, quickly returns home from Coltenhagen, places Canterlot on lockdown, searches her study for clues, interview all personnel on location and then leads a platoon of palace guards to Ponyville upon realizing that Twilight Sparkle is probably in danger. After the fight against Trixie and the Nightmare, it's assumed that she personally brought the seven of them home and put them to bed since the palace guards and cooks still don't know what Harry is and that he's even there. Luna is the one with the maps of Earth and she even leads Harry back down the path towards his world.
Sleep Cute: After their ordeal, the ponies and Harry are taken to Canterlot where they sleep most of the day away on two extra-large mattresses, thanks to Harry's height. When he wakes up, Harry wishes like hell he had a camera — if only to blackmail Rarity and AJ with a picture of them asleep in each other's arms.
Taking the Bullet: Twilight Sparkle teleports in the way of glass shards thrown at Trixie.
Trixie attacks Pinkie with high-speed shards of metal, but Rainbow Dash jumps in front of Pinkie just in time and takes the attack herself.
Would Hurt a Child: Trixie kidnaps Spike and leaves a threatening note out of a paranoid fear that Twilight has caught wind of her schemes. Too bad for Trixie that threatening children is Harry Dresden's Berserk Button.
Animorphism: The Princesses want to award Harry a medal for his services in the previous story, but first they have to make it so that he can walk around without anyone staring at him too hard. That means he has to go native. Naturally, he's a unicorn.
Alas, Poor Villain: The entire Order Triune becomes this. They are sacrificed to a demon by Novel Notion, and while it is karmic when you remember they tried to kill Dresden, it becomes tragic when you realize that they had been misled this entire time, genuinely wanted to protect Equestria, and had been betrayed by one of their own. The way they go is horrible: running for their lives as the circle swallows them, with nothing left of them afterward. The horrified reactions of the Mane 6, and even Harry show this.
Born-Again Immortality: This is essentially what the Order Triune credits their age-old nemesis Obsidian with and what motivates them to kill ponies that look too suspiciously like him.
Brain Bleach: Early on, Harry and Bob have a short argument about finding ponies physically attractive (with Bob being in favor, naturally). After Bob points out "[I'm not the only one who appreciates women of other species]. How do you think centaurs were made anyway?" Harry immediately wishes that mental magic was legal.
Broken Pedestal: After Bob calls out Harry for not killing Arcane Mind when he had the chance and reminds him that he plans to summon He Who Walks Behind again, with Harry killing Justin Dumorne for summoning the demon, Harry believes he has become this for the Mane Six.
"Wait." Twilight said, her brow creasing with worry. "Before we do anything I need to tell you something." All three sets of eyes turned towards her. Twilight lowered her voice just in case anypony from the small crowd watching them had ulterior motives. "This may sound unbelievable, but there's a group of ponies that's planning to kill you, Blackstone." Blackstone starts laughing.
Carnivore Confusion: This gets him in trouble since, even though he's safely changed into a pony and thus has no current cravings for meat, the Order Triune overhear him talking about the issue to Bob.
Damsel out of Distress: The Order Triune captures Twilight. She overcomes their brainwashing and later figures out how to disable the magic-inhibitor they placed on her.
Dangerously Genre Savvy: Novel Notion was able to fool and sacrifice the entire Order Triune to summon a demon. After doing so, he doesn't monologue because he knows the ponies were merely stalling for time, so he used some Order spies in the Royal Guard to make sure they would never get there in time. He knows his magic circle matches that of Harry and the Mane 6, so he takes the Mane 6's family hostage to force them to surrender the Elements of Harmony. Unfortunately, he didn't forsee Princess Celestia disguising herself as Luna, and the real Princess Luna arriving to free the hostages. Still, he proves himself to be quite dangerous.
Harry: We’d dropped plenty of opportunities for him to monologue, but he wasn’t taking the bait. Just my luck to run into a guy who actually followed the Evil Overlord List in a world where they’d never even heard of it.
Didn't See That Coming: In chapter 21 Harry warns the others about relying too much on the plan, since plans don't usually survive contact with the enemy. Neither the heroes' nor the villains' plans work out perfectly thanks to the unexpected. The heroes didn't expect Novel Notion feeding the rest of the Order to a second demon. The villains didn't expect that "Luna" was actually Princess Celestia in disguise.
Twilight decides to play this up when she's trying to convince Harry to let her use her transformation spell on him.
When Twilight is kidnapped in False Masks, Harry experiences this again. Princess Celestia is reluctant to let him continue investigating since she believes he might actually kill whoever is responsible. She even acknowledges that he would have every right and reason to do so, but the last murder in Equestria was over 30 years ago and she rather likes Equestria's current murder-free state.
Fatal Flaw: The Order Triune's refusal to believe that Harry/Blackstone isn't Obsidian allows Bookmark to lure them into a demon sacrifice/summoning circle.
Female Gaze: Mares can't stop telling Harry how good he looks as a stallion.
Freudian Excuse: Double Subverted: Novel Notion at first mockingly states "his parents never hugged him" as his excuse for betraying and murdering the entire Order. Then he gives his real reason. He was frustrated with being indoctrinated into the Order with all its secrets and lies, and sought to destroy it as a means of escape.
Fridge Horror: In-universe, Harry's expression becomes dead serious when he sees the bag of poisoned treats apparently kill a Hydra and recalls that Scootaloo and Rainbow Dash nearly ate some.
Lessened somewhat when they later learn that it wasn't poison, just a very powerful sleeping potion.
From Bad to Worse: The assassination attempts on Harry in False Masks get more extreme and less subtle as time passes. A bag of poisoned candy -> "accidents" like a falling anvil -> poisoned pins -> an entire burlap sack of poisoned food -> siccing a Hydra on Harry.-> unleashing HE WHO WALKS BEHIND when he was about to receive an award for his services.
Full Body Disguise: This time around, Twilight uses a spell to temporarily transform Harry into a pony.
The Gadfly: Luna messing with Harry by pretending she's interested in his pony form.
Heroic Sacrifice: Colgate. Dresden isn't sure if it's the most noble or cliche situation he has ever seen.
High-Pressure Emotion: Rainbow Dash becomes what Harry can only describe as "volcanic" when Bob makes a lewd remark to her about "turning tricks". Harry is relieved when a Hydra attacks him.
Ignored Epiphany: The Cutie Mark Crusaders ponder the truth of Dresden's statement that Cutie Marks are not the be-all and end-all of a pony's existence. For all of five seconds.
I Just Want To Be Free: Novel Notion grew up indoctrinated as a member of the Order of Triune and hated every minute of it. The entire plot is his scheme to kill off the Order.
Innocent Innuendo: Twilight, unaware of most humans' social taboo on nudity, instructs Harry to strip down because she has a "surprise" for him (she wants to transform him into a unicorn for the duration of his stay in Equestria), causing Harry to react with a Spit Take and Bob with glee. Twilight is mortified to learn just what her comment sounded like to Harry and Bob.
Jerkass: During his second trip to Equestria, Harry brings Bob, a spirit of air and intellect that resides within a human skull. He remains quiet during Harry's meeting with Twilight until her Innocent Innuendo, at which point he speaks out, terrifying Spike out of his wits. After having a considerable time convincing Spike that Bob was not a ghost and they were not haunted, Bob promptly shouts "Boo!" at him once Spike worked up enough courage to approach the skull.
Bob then makes lewd remarks to Rarity and Rainbow Dash. The former is disgusted, and the latter is so angry and embarrassed that she is moments away from smashing Bob's skull into powder before a Hydra attacks.
Karmic Death: After spending the whole story trying to assassinate Dresden, putting innocents in danger, betraying the kingdom they swore to protect, and summoning He Who Walks Behind (Twice) , the Order Triune itself is betrayed by Novel Notion and sacrificed to a demon rather quickly. Not that it makes the whole thing any less tragic.
Last-Second Word Swap: A variation appears in chapter 7. Harry is talking with Applejack about his suspicion that his cover's been blown. He's about to say that someone has figured out he's not actually a pony — but when the Cutie Mark Crusaders ask how he was going to finish that sentence, he says that someone has figured out that he bleaches his mane.
Bob: You didn’t see her face after you first turned into a pony. I'm surprised she wasn't drooling.
This also causes Harry a great deal of trouble when he finds himself swarmed by adoring mares after very publicly saving the Cutie Mark Crusaders from an accident meant to kill him. One or more of them may have been in on the assassination plot, and he can't tell who it was.
Noodle Incident: Oh, Bob and your unceasing interest in the female fleshy form...
"Everyone at that sorority was a consenting adult and the alcohol was just as much to blame as I was."
Not Brainwashed: Novel Notion denies that he is being influenced by Obsidian. His evil is all him.
Nothing Is Scarier: Harry's enemies in False Masks scare him more than most of the threats he's faced in the past because they refuse to show themselves. An opponent he can't just blast into oblivion deeply unnerves him.
Not-So-Harmless Villain: The Order Triune fail in their undercover attempts to kill Harry. Then they summon He Who Walks Behind and things become more dire.
Novel Notion. At first he appeared to have been another agent of the Order, who was easily cowed by Harry when found out. It turns out he had manipulated the Order to kill Dresden, and later sacrificed almost all of them to the demon, and later threatened to kill the Mane 6's friends and family if they did not surrender the Elements of Harmony.
Only the Worthy May Pass: How the runes in the Order's HQ work. As Bob explains it, it's not in the least reliable or safe.
Pony Sacrifice: In chapter 21, Novel Notion feeds most of the Order of Triune including Arcane Mind to a demon.
Poor Communication Kills: Lots of it. A justified case in chapter 9: the one fact Twilight could reveal to the Order Triune that would prove that Harry isn't Obsidian — that Harry is a human wizard from another dimension whose magic doesn't quite follow the same rules as pony magic — is also the one thing she believes she really needs to keep a secret.
Power Glows: Harry's aura as a unicorn is red-orange. Makes sense considering how much he likes fire.
Precocious Crush: Well probably not so precocious since by pony standards, Twilight's an older teen/young adult, but Twilight develops one on Dresden shortly after he assumes an equine form. Dresden doesn't reciprocate. Dresden also believes that the reason his pony form is such a Chick Magnet is because Twilight subconsciously made him one due to her crush.
Properly Paranoid: After suffering three near-death experiences in chapter 6 of False Masks, Harry believes that someone or something is trying to kill him. He's completely right, as proven by at least two more assassination attempts in the next chapter. After suffering several more assassination attempts in the chapter after that, Harry decides he's not being paranoid enough.
The Order Triune believe they're this. Unfortunately, they're mostly just paranoid.
Reasonable Authority Figure: Princess Celestia. Despite the trouble he caused in Strange Friends, she doesn't blast Harry within an inch of his life and even thinks he should get a medal for all he's done in Equestria. However while she has no intention of stopping Harry from looking for the Order Triune or Twilight, she knows that while he is the definition of Neutral Good in his world, she also knows that if she gave him free rein over the investigation that it would take literally all of his self control to keep from turning whoever kidnapped Twilight into a smoking crater. Celestia genuinely likes Harry but the ponies first, always.
Rescue Romance: Trixie is shaping to be the third in the triangle. Even though Harry refused.
Right for the Wrong Reasons: Vigilant Watch rightly believed that Novel Notion wanted to wipe out the Order. She wrongly believed that he was Obsidian. Novel Notion was simply sick of life in the Order and wanted out.
Shipper on Deck: Bob wants to see Harry and Twilight get it on. Of course, this is Bob. Bob's preferred ship is Anyone Female/Anyone. He's ecstatic when Lyra and Bon-Bon kiss.
Shout-Out: Twilight's calming mantra after she finds out she's been kidnapped strongly echoes the Litany Against Fear from Dune.
The Starscream: Novel Notion at first seemed to be another one of the Order's many spies, as a secretary of Princess Celestia. He knew Harry was never Obsidian, and used that fact to mislead the Order Triune, whom he sacrificed to a demon.
Tall, Dark and Handsome: Harry's pony form "Blackstone". It's a truly unfortunate coincidence that the Order Triune believes that powerful unicorns with dark pelts are Obisidian reborn.
Tampering with Food and Drink: In chapter 5 of False MasksBon-Bon tries to leave a bag of candy laced with poison for Dresden whom she and the other members of an Ancient Tradition believe to be the reincarnation of the Evil Overlord Obsidian. Things take a turn for the worse when Pinkie Pie eats one. Fortunately, she realizes that there's something wrong with the candy and spits it out, though she still feels drowsy afterwards and passes out in the nearest bed — next to Harry.
Reaches new heights in chapter 7 when someone gives Dresden an ENTIRE burlap sack bag's worth of poisoned treats — enough to slowly and fatally poison a fully-grown Hydra.
Though its later revealed It wasn't poison, just a very powerful sleeping herb.
Teeth-Clenched Teamwork: Even after her Heel-Face TurnBon-Bon still doesn't like Dresden and vice-versa. She thinks that Dresden is dangerous even if he isn't Obsidian. She also truly believes the Order are the good guys, considering she has friends and family in it, and she doesn't want Dresden to hurt them. Dresden and Rarity, on the other hoof, would very much like to hurt them since they kidnapped Twilight. It gets so bad that Dresden tricks her into teleporting home with an escape potion because he can't trust her to not betray them after he is forced to attack Bon-Bon's mother in self-defense.
The Reveal Obsidian, whom the Order Triune believe Harry's pony form to be, never resurrected. Unfortunately for the Triune, their true enemy was Novel Notion, who rather than just another mook, was in fact the one who had been stringing them along so he could destroy the Order Triune.
Red Herring: In-universe and out, Obsidian is mentioned so often that no one really considers that he might not have resurrected this time even though there's never been any hard evidence that he has.
Time Skip: False Masks takes place after Blood Rites. Nearly a year has passed on Earth, and two months have passed in Equestria.
Token Good Teammate: Colgate is shaping up to be this for the Order Triune. Mouse seems to like her when she first visits Twilight's home.
Tykebomb: Harry cynically wonders if every member of the Order is one of these after hearing that Bon-Bon was literally born to join the Order. Novel Notion's frustration with being one kicks off the entire plot, culminating in a mostly successful attempt to slaughter the Order.
Vagueness Is Coming: Keen Vision warns Twilight of this, specifically that the coming "darkness" is centered around her and Harry.
Why Did It Have to Be Snakes?: Harry now has a fear of fire thanks to nearly cooking his own hand in canon. He can't even perform the smallest flame magic without sweating nervously, and he is shaken when Spike breathes fire at an enemy.
Bon Bon: You’re a man of iron and blood, stone and fire. Touched by darkness, but not overcome by it. Beaten and damaged, but unbowed. Unrelenting in word and deed, in thought and creed. You would lay siege to Tartarus itself if that’s where Twilight had been taken. And all because she’s your friend. Because you would do anything to keep her safe. Because you care.
Harry gets in on it in chapter 14 while talking to Trixie:
Harry:"You're right, I have no idea what happened to you. But I can tell you this, you aren't going to fix it with self-pity. And if you knew anything about the pony I'm trying to save, you'd never tell us to just leave you." Trixie: "That's not−" Harry:"No, I'm talking now. I know you said you don't remember much about that night, but let me tell you something, Trixie. I tried to kill you after the girls blasted you with the Harmony ray. There was a demon running around, and it certainly influenced me, but I had control of my own actions. I wanted you dead, because of everything you'd done to my friends and everything I feared you would do in the future. The girls tried to convince me not to do it, and eventually, when I refused to see reason, they fought me. To protect you. The demon stoked my rage and I returned the favor. I won. I beat all of them and then I went to kill you. Twilight teleported in front of my attack, trying to save you, and it nearly killed her. She went to death's door to keep your sorry ass safe even after everything you had done to her. I will be damned before I let her pain and courage go to waste. I am not letting you lie down and die. You are coming with us, whether you like it or not."
Would Not Hurt A Child: In False Masks, whoever is trying to kill Harry is considerate enough to shield the Cutie Mark Crusaders from being killed by the runaway wagon they hijacked to kill Dresden. However, said assassin was also willing to use them as bait in the first place to keep Dresden from just running away. As well as dole out a large amount of tainted treats, far more then Harry could eat on his own, with the foals around in plain sight of it, and which they almost instantly try to eat some of.
this dichotomy of both protecting, and endangering the foals is what leads Harry to believe there is either two groups, or two separate factions of the same group, each trying to off him separately. With one taking more care to avoid collateral damage then the other.